I presume it was no big deal for warships as, the way I understand it, they were dry docked and beached as often as possible, but I can't imagine merchant ships having such a luxury, or lasting long without any such treatment at all...
So did they use copper, like later ships, something else, or was fouling not as big problem as I think for them for some other reason?
I can help for shipworms, at least. Those require saltwater. They are a bivalve, like a clam or oyster, and are filter feeders, constantly pumping water in and out. Freshwater kills them, so the old solution to keeping a hull free of them was to take the boat up a river until the salinity dropped, and anchor it for a while.